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Web-accessible scientific workflow system for performance monitoring.

We describe the design and implementation of a web-accessible scientific workflow system for environmental performance monitoring. This workflow environment integrates distributed automated data acquisition with server side data management and information visualization through flexible browser-based data access tools. Component technologies include a rich browser-based client, a back-end server for methodical data processing, user management, and result delivery, and third party applications which are invoked by the back-end using web services. This environment allows for reproducible, transparent result generation by a diverse user base, and provides a seamless integration between data selection, analysis applications, and result delivery. This workflow system has been implemented for several sites and monitoring systems with different degrees of complexity.

Databases, Factual↗

Automated liquid handling and high-throughput preparation of polymerase chain reaction-amplified DNA for microarray fabrication.

Genome-wide studies of gene expression and transcription factor-binding sites using DNA microarrays are leading to new systems level insights. The massively parallel nature of microarrays presents technical challenges: fabricating high-quality microarrays at the front end and data analysis and interpretation downstream. A principal challenge in fabricating microarrays is preparation of the DNA samples. This is particularly the case for polymerase chain reaction-amplified DNA samples. The challenge is to scale up efficiently to high-throughput preparation of tens of thousands of DNA samples while ensuring a uniform high quality. This chapter outlines strategic considerations, including automated liquid handling and workflow development to maximize efficiency, and quality control (QC) measures to ensure uniform quality. The protocols are presented with commentary to illustrate their logic and specific techniques. These principles and techniques are extensible to other high-throughput molecular biological applications.

Animals↗

[Quantification of pulmonary emphysema in multislice-CT using different software tools].

PURPOSE: The data records of thin-section MSCT of the lung with approx. 300 images are difficult to use in manual evaluation. A computer-assisted pre-diagnosis can help with reporting. Furthermore, post-processing techniques, for instance, for quantification of emphysema on the basis of three-dimensional anatomical information might be improved and the workflow might be further automated. MATERIALS AND METHODS: The results of 4 programs (Pulmo, Volume, YACTA and PulmoFUNC) for the quantitative analysis of emphysema (lung and emphysema volume, mean lung density and emphysema index) of 30 consecutive thin-section MSCT datasets with different emphysema severity levels were compared. The classification result of the YACTA program for different types of emphysema was also analyzed. RESULTS: Pulmo and Volume have a median operating time of 105 and 59 minutes respectively due to the necessity for extensive manual correction of the lung segmentation. The programs PulmoFUNC and YACTA, which are automated to a large extent, have a median runtime of 26 and 16 minutes, respectively. The evaluation with Pulmo and Volume using 2 different datasets resulted in implausible values. PulmoFUNC crashed with 2 other datasets in a reproducible manner. Only with YACTA could all graphic datasets be evaluated. The lung volume, emphysema volume, emphysema index and mean lung density determined by YACTA and PulmoFUNC are significantly larger than the corresponding values of Volume and Pulmo (differences: Volume: 119 cm(3)/65 cm(3)/1 %/17 HU, Pulmo: 60 cm(3)/96 cm(3)/1 %/37 HU). Classification of the emphysema type was in agreement with that of the radiologist in 26 panlobular cases, in 22 paraseptalen cases and in 15 centrilobular emphysema cases. CONCLUSION: The substantial expenditure of time obstructs the employment of quantitative emphysema analysis in the clinical routine. The results of YACTA and PulmoFUNC are affected by the dedicated exclusion of the tracheobronchial system. These fully automatic tools enable not only fast quantification without manual interaction, but also a reproducible measurement without user dependence.

Adolescent↗

How healthcare IT can address the nursing shortage.

But if applied correctly, IT can play an important role in redefining the way nursing is conducted. It can do so by introducing flexible models of nursing education to increase the pool of qualified nursing professionals; automating and standardizing nursing workflows; eliminating paperwork; supporting patient care delivery models that address the needs of an older workforce; establishing point-of-care clinical decision support tools to improve patient safety; and making health, wellness, and patient education information available. If healthcare IT solutions are deployed in direct response to nursing's ills, particularly job dissatisfaction, the positive image of nursing can be restored, once again making it a career of choice. IT can further reverse the tide of nursing defections, which continually drain the healthcare industry of experienced and dedicated professionals. Finally, both individually and collectively, healthcare IT technologies can reorient nursing activity back towards its principal role of delivering quality patient care.

Hospital Information Systems↗

A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics.

A new matrix-assisted laser-desorption/ionization time-of-flight/time-of-flight mass spectrometer with the novel "LIFT" technique (MALDI LIFT-TOF/TOF MS) is described. This instrument provides high sensitivity (attomole range) for peptide mass fingerprints (PMF). It is also possible to analyze fragment ions generated by any one of three different modes of dissociation: laser-induced dissociation (LID) and high-energy collision-induced dissociation (CID) as real MS/MS techniques and in-source decay in the reflector mode of the mass analyzer (reISD) as a pseudo-MS/MS technique. Fully automated operation including spot picking from 2D gels, in-gel digestion, sample preparation on MALDI plates with hydrophilic/hydrophobic spot profiles and spectrum acquisition/processing lead to an identification rate of 66% after the PMF was obtained. The workflow control software subsequently triggered automated acquisition of multiple MS/MS spectra. This information, combined with the PMF increased the identification rate to 77%, thus providing data that allowed protein modifications and sequence errors in the protein sequence database to be detected. The quality of the MS/MS data allowed for automated de novo sequencing and protein identification based on homology searching.

Amino Acid Sequence↗

Digital doctoring.

PROBLEM: Clinicians and support staff struggled with the need to carefully track the clinical information flowing through the practice in a paper-based system, while at the same time providing the best possible patient care. SOLUTION: A browser-based software application automated the practice's complete workflow system--from scheduling and referrals management to lab and radiology results. RESULTS: Consolidated information and workflow management means everyone spends less time chasing paper and more time caring for patients. KEYS TO SUCCESS: Because today's information technology moves in a rapid sequence of incremental innovations, you can't wait for a "final" solution before you begin to automate.

Ambulatory Care Information Systems↗

Intraoperative Iso-C C-arm navigation in craniospinal surgery: the first 60 cases.

OBJECTIVE: The intraoperative Iso-C C-arm (Siremobil Iso-C 3D; Siemens Medical Solutions, Erlangen, Germany) provides a unique ability to acquire and view multiplanar three-dimensional images of intraoperative anatomy. Registration for intraoperative surgical navigation may be automated, thus simplifying the operative workflow. METHODS: Iso-C C-arm intraoperative fluoroscopy acquires 100 images, each of which must be 1.8 degrees in a circumferential fashion about an "isocentric" point in space. The system generates a high-resolution isotropic three-dimensional data set that is available immediately after the 90-second C-arm rotation. The data set is ported to the image-guided workstation, registration is immediate and automated, and the surgeon can navigate with millimetric accuracy. The authors prospectively examined data from the initial 60 patients examined with the Iso-C, among whom were cases of anterior and posterior spinal instrumentation from the occiput to the sacrum. Percutaneous and minimally invasive spinal and cranial procedures were also included. RESULTS: Automated registration for image-guided navigation was attainable for anterior and posterior cases from the cranial base and entire spine. In most cases, intraoperative postprocedural imaging with the Iso-C mitigated the need for postoperative imaging. CONCLUSION: Intraoperative Iso-C three-dimensional scanning allows real-time feedback during cranial base and spinal surgery and during procedures involving instrumentation. In most cases, it obviates the need for postoperative computed tomography. Its usefulness is in its simplicity, and it can be easily adapted to the operating room workflow. When coupled with intraoperative navigation, this new technology facilitates complex neurosurgical procedures by improving the accuracy, safety, and time of surgery.

Adolescent↗

Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System.

In this review we describe the principles, protocols, and applications of two commercially available SNP genotyping platforms, the TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Combined, these two technologies meet the requirements of multiple SNP applications in genetics research and pharmacogenetics. We also describe a set of SNP selection tools and validated assay resources which we developed to accelerate the cycle of experimentation on these platforms. Criteria for selecting the more appropriate of these two genotyping technologies are presented: the genetic architecture of the trait of interest, the throughput required, and the number of SNPs and samples needed for a successful study. Overall, the TaqMan assay format is suitable for low- to mid-throughput applications in which a high assay conversion rate, simple assay workflow, and low cost of automation are desirable. The SNPlex Genotyping System, on the other hand, is well suited for SNP applications in which throughput and cost-efficiency are essential, e.g., applications requiring either the testing of large numbers of SNPs and samples, or the flexibility to select various SNP subsets.

Gene Frequency↗

Simulation analysis of pneumatic tube systems.

Pneumatic tube systems play an important material handling role in many hospitals. These systems are costly and complex to design and operate, yet little exists in the way of analytical methodologies for them. We present a decision support framework based on defining relevant system performance metrics, traffic analysis reporting, as well as discrete event simulation modeling. We have used this approach to analyze numerous pneumatic tubes systems in the United States and present a representative case study from a large tertiary care hospital. Our general approach can be generalized to other computer controlled hospital operational systems such as elevators, track vehicles, automatic guided vehicles, workflow enabled processes, and laboratory automation systems.

Computer Simulation↗

AI'm Here to Help: Enhancing Laboratory Genetic Counseling with Artificial Intelligence.

BACKGROUND: Artificial intelligence (AI) is transforming the fields of genetics and genetic counseling, enhancing both clinical and laboratory practices. The rise of AI technologies has drawn attention to their potential impact on genetic counseling, particularly in patient diagnosis and the counseling processes. CONTENT: In the laboratory, AI plays a critical role in improving communication between laboratory genetic counselors and healthcare providers by automating routine tasks and optimizing workflows. These advancements allow genetic counselors to dedicate more time to addressing complex inquiries, improving genetic test selection, and helping providers interpret genetic test results. As AI continues to integrate into laboratory genetic counseling practice, it presents both opportunities and challenges. At the time of submission, there is a large knowledge gap regarding AI and its application to laboratory genetic counseling, given the lack of published information on this topic. SUMMARY: This article summarizes existing literature, the history and current applications of AI in laboratory genetic counseling, examines its benefits and limitations, and explores future directions for its implementation in the field.

Humans↗

A workflow-based approach to virtual patient record security.

Virtual patient records provide a means for integrated access to patient information that may be scattered around different healthcare organizations (or hospital departments). As Intranets provide, among others, secure access to medical information, they constitute an appropriate technological infrastructure for a virtual patient record implementation. In such cases, a security policy can be enforced by combining the security features of the Intranet with the security features of the intraorganizational systems. However, when a workflow system is implemented to automate interorganizational healthcare processes, an additional security layer is needed. An authorization architecture that serves this purpose is presented in this paper.

Computer Communication Networks↗

An open-source clinical bioinformatics pipeline for real-world NGS implementation: translating genomic variants into actionable treatment strategies in oncology.

BACKGROUND: Next-Generation Sequencing (NGS) has become a cornerstone technology in clinical practice, yet its adoption presents significant challenges. Physicians and oncologists must manage vast amounts of genome-scale data and transform it into actionable insights for complex decision-making. While commercial systems exist to synthesize data from NGS experiments into clinical reports, many are hindered by limitations such as closed-source designs that restrict transparency and customization. Additionally, some fail to leverage publicly available genomic databases, missing opportunities to integrate valuable external data. Furthermore, the rigidity of many tools in accommodating diverse NGS panels limits their applicability across varied clinical scenarios. METHODS: To address these limitations, we developed OncoReport, an open-source tool that generates comprehensive reports from NGS analyses. By integrating publicly accessible databases, OncoReport provides a robust, user-friendly environment equipped with essential tools for NGS analysis. This design aims to enhance data interpretation and support informed clinical decision-making. RESULTS: Rigorous testing has demonstrated OncoReport’s effectiveness in producing detailed, actionable reports that are clear and easy to use. By automating key aspects of the workflow, the tool significantly reduces manual effort and expedites the synthesis and interpretation of NGS results, making genomic insights more accessible to clinicians. CONCLUSION: OncoReport offers a transparent, flexible, and efficient framework for clinicians to analyze and apply genomic data in patient care. By streamlining workflows and leveraging open-source principles, it empowers healthcare professionals to make informed, data-driven decisions. OncoReport is freely available at https://oncoreport.atlas.dmi.unict.it, with source code and issue tracking on GitHub: https://github.com/knowmics-lab/oncoreport .

Humans↗

Workflow optimization: current trends and future directions.

In an attempt to maximize productivity within the medical imaging department, increasing importance and attention is being placed on workflow. Workflow is the process of analyzing individual steps that occur during a single event, such as the performance of an MRI exam. The primary focus of workflow optimization within the imaging department is automation and task consolidation, however, a number of other factors should be considered including the stochastic nature of the workload, availability of human resources, and the specific technologies being employed. The purpose of this paper is to determine the complex relationship that exists between information technology and the radiologic technologist, in an attempt to determine how workflow can be optimized to improve technologist productivity. This relationship takes on greater importance as more imaging departments are undergoing the transition from film-based to filmless operation. A nationwide survey was conducted to compare technologist workflow in film-based and filmless operations, for all imaging modalities. The individual tasks performed by technologists were defined, along with the amount of time allocated to these tasks. The index of workflow efficiency was determined to be the percentage of overall technologist time allocated to image acquisition, since this is the primary responsibility of the radiologic technologist. Preliminary analysis indicates technologist workflow in filmless operation is enhanced when compared with film-based operation, for all imaging modalities. The specific tasks that require less technologist time in filmless operation are accessing data and retake rates (due to both technical factors and lost exams). Surprisingly, no significant differences were reported for the task of image processing, when comparing technologist workflow in film-based and filmless operations. Additional research is planned to evaluate the potential workflow gains achievable through workflow optimization software, improved systems integration, and automation of advanced image processing techniques.

Efficiency, Organizational↗

Guideline-based careflow systems.

This paper describes a methodology for achieving an efficient implementation of clinical practice guidelines. Three main steps are illustrated: knowledge representation, model simulation and implementation within a health care organisation. The resulting system can be classified as a 'guideline-based careflow management system'. It is based on computational formalisms representing both medical and health care organisational knowledge. This aggregation allows the implementation of a guideline, not only as a simple reminder, but also as an 'organiser' that facilitates health care processes. As a matter of fact, the system not only suggests the tasks to be performed, but also the resource allocation. The methodology initially comprehends a graphical editor, that allows an unambiguous representation of the guideline. Then the guideline is translated into a high-level Petri net. The resources, both human and technological necessary for performing guideline-based activities, are also represented by means of an organisational model. This allows the running of the Petri net for simulating the implementation of the guideline in the clinical setting. The purpose of the simulation is to validate the careflow model and to suggest the optimal resource allocation before the careflow system is installed. The final step is the careflow implementation. In this phase, we show that the 'workflow management' technology, widely used in business process automation, may be transferred to the health care setting. This requires augmenting the typical workflow management systems with the flexibility and the uncertainty management, typical of the health care processes. For illustrating the proposed methodology, we consider a guideline for the management of patients with acute ischemic stroke.

Artificial Intelligence↗

Integration of a rapid automated solubility classification into early validation of hits obtained by high throughput screening.

Besides the structural verification of hits generated by high throughput screening also the determination of physicochemical properties is essential for an efficient lead identification. Especially solubility is fundamental for the correct planning and interpretation of experiments. We describe the set up of a fast automated solubility test within our existing workflow for hit validation to assure compound identity and purity. 384-Well plates with hit validation compound solution are used for analysis employing liquid chromatography and mass spectrometry (LC/MS). The remaining compound solution was used for a fast automated solubility classification employing a nephelometer integrated into a Tecan robotic workstation. Thereby 9000 compounds were classified as poorly- and well-soluble. This rapid and simple test does not require any additional amount of sample or sample processing than before but provides additional information on the hits at an early stage of lead identification. Validated by a more detailed nephelometric analysis for 500 out of the 9000 compounds in different buffer systems this simple test has shown to produce relevant data.

Automation↗

Workflow improvement and impact of the new Beckman Coulter LH 1500 high throughput automated hematology workcell.

Our core laboratory at St. Joseph's Medical Center (SJMC) recently installed the new Beckman Coulter LH 1500 fully automated hematology workcell. Like many laboratories in North America and other parts of the world, we are under significant pressure to improve productivity, reduce costs, and improve service provision to our hospital and clinician bases. The difficulty of meeting this challenge is often further compounded by an increasing shortage of qualified technologist personnel. We recently reported on the significant productivity gains with the introduction of the LH 750 hematology system into the core laboratory, including a 23% reduction in slide review rate, automation of reticulocyte and nucleated red blood cell counts, and an 82% increase in the pass-through rate. Evolution to the next stage of automation has come much quicker than anticipated owing to a steep rise in workload and an ever increasing shortage of trained and experienced technologists to fill vacancies in the 24-hour core laboratory operation. We chose to upgrade our LH 750 analyzers to the newly introduced LH 1500 hematology workcell in order to cope with the increased workload and shortage of available experienced hematology technologists. The LH 1500 is a compact, high throughput, fully automated hematology workcell. It is designed to automate all manual process and handling steps associated with hematology analyses, including sample sorting, loading and unloading of cassettes, automatic rerun and reflex testing, sample storage, and tracking of samples. The LH 1500 is comprised of a minimum of 2, and up to 4, LH 750 instruments (with or without integrated slidemaker/stainers). The instruments are bidirectionally interfaced and linked to a fully automated conveyor track, specimen inlet and outlet stations, a sample stockyard, and a line controller. The configuration we chose at SJMC incorporates 1 LH 750 and 1 LH 755. We report that the upgrade to the LH 1500 was a relatively straightforward process and required no redesign of the core laboratory. Based on our evaluation, we estimate cost savings with the LH 1500 of between three quarters to 1 full-time equivalent, which eliminated or decreased many manual handling steps. In addition, this increase in efficiency has freed up our technologist resources to concentrate on the more difficult and clinically important samples. This is the first published report on the new LH 1500 hematology workcell. Our research indicates that the LH 1500 is the first hematology workcell to offer hematology laboratories the next level of automation and virtually eliminate preanalytical and postanalytical sample handling and sorting. For core laboratories and high-throughput hematology laboratories that face similar pressures to ours, the LH 1500 would appear as an attractive solution to maximize hematology productivity and improve service delivery.

Automation↗

A sum greater than its parts: a lesson in clinical-financial integration.

Clinical-financial integration at St. Vincent's Medical Center involved three basic initiatives: A cultural change initiative to educate individuals throughout the hospital about their contributions to the hospital's financial health. An IT initiative to take full advantage of the capability of St. Vincent's enterprisewide clinical IT system to support an integrated, clinically automated revenue cycle. A staffing initiative to realign staff roles and workflows in financial services departments to capitalize on the IT automation.

Connecticut↗

Design requirements for radiology workstations.

This article stresses the importance of capturing feedback from representative users in the early stages of product development. We present our solution to producing quality requirement specifications for radiology workstations, specifications that remain valid over time because we successfully anticipated the industry trends and the user's needs. We present the results from a user study performed in December 1999 in a radiology clinic equipped with state-of-the-art Picture Archiving and Communications Systems (PACS) and imaging scanners. The study involved eight radiologists who answered questions and provided comments on three complementary research topics. First, we asked our subjects to enumerate the advantages and the disadvantages for both softcopy and hardcopy reading. We identified the two major factors for productivity improvement through the use of PACS workstations: workflow re-engineering and process automation. Second, we collected radiologist feedback on the use of hanging protocols (HPs). The results indicated the high importance of automatic image organization through HPs, with the potential effect of reducing the interpretation time by 10-20%. Our subjects estimated that 10-15 HPs would cover about 85%-95% of the regular radiological examinations. Third, we investigated the impact of the display devices on the radiologist's workflow. Our results indicated that the number and the properties of the monitors is a modality-specific requirement. The main results from this study on key functional requirements for softcopy interpretation only recently were incorporated in most of the current, successful PACS workstations.

Attitude of Health Personnel↗